User: Rory Stark

gravatar for Rory Stark
Rory Stark2.5k
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2,450
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Location:
CRUK, Cambridge, UK
Last seen:
4 days, 4 hours ago
Joined:
5 years, 4 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 435 results • page 1 of 44 • next >
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Comment: C: Changing box plot font sizes for axes and labels in DiffBind
... Bug has been logged and will be fixed. -R ...
written 4 days ago by Rory Stark2.5k
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Answer: A: getting DiffBind full result list
... You can get stats for all the peaks by setting th=1 in the call to dba.report(). It's worth noting that it is not necessarily the case that peaks with higher FDR values are not changing, rather that there is insufficient evidence to be confident that they did change (potentially due to e.g. inadequ ...
written 11 days ago by Rory Stark2.5k
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Answer: A: change x- and y-axis limit within dba.plotVolcano in DiffBind
... dba.plotVocano() uses ggplot internally, so ylim() doesn'y work. There is no easy way to change the behavior of dba.plotVolcano(). If you assign the return value of the call to dba.plotVolcano(), you will get a GRanges object with all the data you need to make your own plots. For example: > da ...
written 14 days ago by Rory Stark2.5k
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Answer: A: DiffBind question on adb.contrast
... One or both of the masks (either H3K4me3$masks$V1 or H3K4me3$masks$S1) is equal to NULL. You can check the valid mask names as follows: > names(H3K4me3$masks) It is also worth noting that the minMembers parameter only applies when you do not specify the groups explicitly, so in this case it wil ...
written 17 days ago by Rory Stark2.5k
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Answer: A: DiffBind Change of Metadata once dba.counts have been called
... While not part of the "official" interface, you can access the metadata fields directly: myDBA$class[DBA_TISSUE, ] myDBA$class[DBA_FACTOR, ] myDBA$class[DBA_CONDITION, ] myDBA$class[DBA_TREATMENT, ] myDBA$class[DBA_REPLICATE, ] You can set these to vectors of character strings to change the value ...
written 26 days ago by Rory Stark2.5k
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Answer: A: Counting reads in fixed width peaks with DiffBind::dba.count without re-centerin
... If you do not want to re-center the peaks, there is no need to use the summits parameter. You can use the peaks parameter to specify the exact intervals you want: > dba_cnt <- dba.count(dba, peaks=Peaks) Cheers- Rory ...
written 26 days ago by Rory Stark2.5k
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Answer: A: Combine separate dba objects into the one
... You can use dba.peakset() to add all the peaks from one DBA object to another. If you want to add the peaks from myDBA2 to myDBA1, the call is: > myDBA3 <- dba.peakset(myDBA1,peaks=myDBA2) Cheers- Rory ...
written 26 days ago by Rory Stark2.5k
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Comment: C: DiffBind Analysis with more than 2 samples?
... This is a new question, not a comment on the original quesiton, and should be logged as such. Given a set of DB sites from a contrast, you can see how all the samples cluster, whether or not they are in the contrast, by setting the mask parameter to eg dba.plotHeatmap() and dba.plotPCA(). So if you ...
written 8 weeks ago by Rory Stark2.5k
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Comment: C: How to extract overlapping and unique peaks from the Venn Diagram to a csv forma
... Actually you can just call write.csv() on a GRanges object. You will get a column with the strand, which you may not want. Another way is to convert a GRanges to a data.frame by calling data.frame(myGRanges), then write that out with write.csv() including/deleting the columns you are/aren't interes ...
written 8 weeks ago by Rory Stark2.5k
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Comment: C: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
... I'll log that suggestion down as a feature request, it may appear at some point... ...
written 8 weeks ago by Rory Stark2.5k

Latest awards to Rory Stark

Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Scholar 12 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Scholar 12 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Scholar 12 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 12 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 12 months ago, created a question with more than 1,000 views. For a diffBind problem
Popular Question 12 months ago, created a question with more than 1,000 views. For diffbind
Scholar 12 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Popular Question 12 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 12 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Guru 13 months ago, received more than 100 upvotes.
Popular Question 13 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 13 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 14 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.2 years ago, created an answer that has been accepted. For A: DiffBind matrix of values

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